Abstract The present paper investigates the transverse vibration of a non-uniform axially functionally graded Timoshenko beam with cross-sectional and material properties varying in the beam length direction. The Chebyshev collocation method is used to spatially discretize the governing partial differential equations of motion of the beam into time-dependent ordinary differential equations in terms of Chebyshev differentiation matrices. An algebraic eigenvalue equation in matrix form is then formed to study the free vibration behavior of non-uniform axially functionally graded Timoshenko beams. Several results of natural frequencies of the beams are evaluated and compared with those in the published literature to assure the accuracy of the proposed model. The effects of taper ratio, material graded index, slenderness ratio, material compositions and restraint types on the natural frequencies of tapered axially functionally graded Timoshenko beams are examined.